OpenPlant Fund supports open source multi-fluorescence imaging system published in PLOS One

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study supported by the OpenPlant Fund, Isaac Nuñez, Tamara Matute and collaborators describe a multi-fluorescence imaging system that integrates low-cost and open-source hardware, software and genetic resources.

The illumination and optics system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics and the box design and flexible focusing allows imaging in scales ranging from single colonies to entire plates. The team also developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, they screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins for 3-channel fluorescent imaging.

Open source Python code was developed to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, the team tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology.

Isaac Nuñez appreciated the opportunity to work on the project with the support of OpenPlant: “OpenPlant funds were important because we are generating a real impact in research and teaching through interdisciplinarity. This project not only introduced us to new modes of work based on good practices, documentation and open source licensing but also allowed us to learn from different fields such as open hardware, design, FOSS and advanced DNA fab methods.”

In order to highlight the benefits of employing an open framework, the team formed an industry partnership with the Open Source company Backyard Brains (TM), which has significant experience in creating and distributing open educational and research technology for neuroscience in Latin America and worldwide (backyardbrains.com, backyardbrains.cl). In collaboration, the team assessed the potential use of their imaging statuon in a high school environment.  Author Tamara Matute explained “We have been able to use these resources in workshops in high schools, community spaces and cultural centres; and implement advanced practicals to teach in vitro synbio, DNA fab and microbiology. The open source and low cost nature of the resources has allowed citizens to better understand the principles behind gene expression analysis and modelling”

Together, their results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. The paper was selected as Editor's Pick for the PLOS Open Source Toolkit Channel in December 2017.

Original Publication: Nuñez, I., Matute, T., Herrera, R., Keymer, J., Marzullo, T., Rudge, T., & Federici, F. (2017). Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering. PLOS One, 12(11), e0187163.

Synthetic Biology and the Senses: volunteers wanted for Cambridge Science Festival

Synthetic biology can bring cutting edge biotechnology into everyday experiences through people's senses by harnessing the wonderful variety of colours, scents, tastes and textures produced in nature. We are looking for enthusiastic volunteers and interactive exhibits or colourful posters to illustrate the theme of 'Synthetic Biology and the Senses' at the Cambridge Science Festival Life Science Marquee on Sat 17 March 2018.

'Synthetic Biology and the Senses' is a joint exhibit by OpenPlant and the SynBio SRI and will run 10:00-16:00 on Sat 17 March 2018 on the Downing Site Lawn, with volunteers required before and after for set-up and packing down. 

We are looking for volunteers to help out and talk to visitors as well as proposing activies or exhibits of their own. In 2017 we featured exhibits including:

• Bioluminescent bacteria

• Fabrics dyed with synthetic ink from bacteria

• Micro-organisms expressing plant metabloic pathways to produce rose and patchouli scents

• Design-a-plant

• Dave the DNA Robot

 We require volunteers for various times of the day and would be very happy to have 4 people at the exhibit at all times. Two hour slots are available and volunteers can stay as long as they wish. Lunch and Science Festival T-Shirt provided!

Please register via this form.

Report highlights opportunities and risks associated with synthetic biology and bioengineering

Human genome editing, 3D-printed replacement organs and artificial photosynthesis – the field of bioengineering offers great promise for tackling the major challenges that face our society. But as a new article out today highlights, these developments provide both opportunities and risks in the short and long term.

Rapid developments in the field of synthetic biology and its associated tools and methods, including more widely available gene editing techniques, have substantially increased our capabilities for bioengineering – the application of principles and techniques from engineering to biological systems, often with the goal of addressing 'real-world' problems.

In a feature article published in the open access journal eLife, an international team of experts led by Dr Bonnie Wintle and Dr Christian R. Boehm from the Centre for the Study of Existential Risk at the University of Cambridge, capture perspectives of industry, innovators, scholars, and the security community in the UK and US on what they view as the major emerging issues in the field. The participants included several OpenPlant researchers and members of the management team.

Dr Wintle says: “The growth of the bio-based economy offers the promise of addressing global environmental and societal challenges, but as our paper shows, it can also present new kinds of challenges and risks. The sector needs to proceed with caution to ensure we can reap the benefits safely and securely.”

The report is intended as a summary and launching point for policy makers across a range of sectors to further explore those issues that may be relevant to them.

Among the issues highlighted by the report as being most relevant over the next five years are:

Artificial photosynthesis and carbon capture for producing biofuels

If technical hurdles can be overcome, such developments might contribute to the future adoption of carbon capture systems, and provide sustainable sources of commodity chemicals and fuel.  

Enhanced photosynthesis for agricultural productivity

Synthetic biology may hold the key to increasing yields on currently farmed land – and hence helping address food security – by enhancing photosynthesis and reducing pre-harvest losses, as well as reducing post-harvest and post-consumer waste.

Synthetic gene drives

Gene drives promote the inheritance of preferred genetic traits throughout a species, for example to prevent malaria-transmitting mosquitoes from breeding. However, this technology raises questions about whether it may alter ecosystems, potentially even creating niches where a new disease-carrying species or new disease organism may take hold.

Human genome editing

Genome engineering technologies such as CRISPR/Cas9 offer the possibility to improve human lifespans and health. However, their implementation poses major ethical dilemmas. It is feasible that individuals or states with the financial and technological means may elect to provide strategic advantages to future generations.

Defence agency research in biological engineering

The areas of synthetic biology in which some defence agencies invest raise the risk of ‘dual-use’. For example, one programme intends to use insects to disseminate engineered plant viruses that confer traits to the target plants they feed on, with the aim of protecting crops from potential plant pathogens – but such technologies could plausibly also be used by others to harm targets.

In the next five to ten years, the authors identified areas of interest including:

Regenerative medicine: 3D printing body parts and tissue engineering

While this technology will undoubtedly ease suffering caused by traumatic injuries and a myriad of illnesses, reversing the decay associated with age is still fraught with ethical, social and economic concerns. Healthcare systems would rapidly become overburdened by the cost of replenishing body parts of citizens as they age and could lead new socioeconomic classes, as only those who can pay for such care themselves can extend their healthy years.

Microbiome-based therapies

The human microbiome is implicated in a large number of human disorders, from Parkinson’s to colon cancer, as well as metabolic conditions such as obesity and type 2 diabetes. Synthetic biology approaches could greatly accelerate the development of more effective microbiota-based therapeutics. However, there is a risk that DNA from genetically engineered microbes may spread to other microbiota in the human microbiome or into the wider environment.

Intersection of information security and bio-automation

Advancements in automation technology combined with faster and more reliable engineering techniques have resulted in the emergence of robotic 'cloud labs' where digital information is transformed into DNA then expressed in some target organisms. This opens the possibility of new kinds of information security threats, which could include tampering with digital DNA sequences leading to the production of harmful organisms, and sabotaging vaccine and drug production through attacks on critical DNA sequence databases or equipment.

Over the longer term, issues identified include:

New makers disrupt pharmaceutical markets

Community bio-labs and entrepreneurial startups are customizing and sharing methods and tools for biological experiments and engineering. Combined with open business models and open source technologies, this could herald opportunities for manufacturing therapies tailored to regional diseases that multinational pharmaceutical companies might not find profitable. But this raises concerns around the potential disruption of existing manufacturing markets and raw material supply chains as well as fears about inadequate regulation, less rigorous product quality control and misuse.

Platform technologies to address emerging disease pandemics

Emerging infectious diseases—such as recent Ebola and Zika virus disease outbreaks—and potential biological weapons attacks require scalable, flexible diagnosis and treatment. New technologies could enable the rapid identification and development of vaccine candidates, and plant-based antibody production systems.

Shifting ownership models in biotechnology

The rise of off-patent, generic tools and the lowering of technical barriers for engineering biology has the potential to help those in low-resource settings, benefit from developing a sustainable bioeconomy based on local needs and priorities, particularly where new advances are made open for others to build on.

Dr Jenny Molloy comments: “One theme that emerged repeatedly was that of inequality of access to the technology and its benefits. The rise of open source, off-patent tools could enable widespread sharing of knowledge within the biological engineering field and increase access to benefits for those in developing countries.”

Professor Johnathan Napier from Rothamsted Research adds: “The challenges embodied in the Sustainable Development Goals will require all manner of ideas and innovations to deliver significant outcomes. In agriculture, we are on the cusp of new paradigms for how and what we grow, and where. Demonstrating the fairness and usefulness of such approaches is crucial to ensure public acceptance and also to delivering impact in a meaningful way.”

Dr Christian R. Boehm concludes: “As these technologies emerge and develop, we must ensure public trust and acceptance. People may be willing to accept some of the benefits, such as the shift in ownership away from big business and towards more open science, and the ability to address problems that disproportionately affect the developing world, such as food security and disease. But proceeding without the appropriate safety precautions and societal consensus—whatever the public health benefits—could damage the field for many years to come.”

The research was made possible by the Centre for the Study of Existential Risk, the Synthetic Biology Strategic Research Initiative (both at the University of Cambridge), and the Future of Humanity Institute (University of Oxford). It was based on a workshop co-funded by the Templeton World Charity Foundation and the European Research Council under the European Union’s Horizon 2020 research and innovation programme. 

Reference
Wintle, BC, Boehm, CR et al. A transatlantic perspective on 20 emerging issues in biological engineering. eLife; 14 Nov 2017; DOI: 10.7554/eLife.30247

Link to original piece on University News

Hear OpenPlant Coordinator Dr Jenny Molloy discuss the work on BBC Radio 4 'Inside Science' 

The text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

Image Credit: Reaching for the Sky
Susanne Nilsson

Open technology and democratisation of synthetic biology features on BBC Radio 4 'Inside Science'

The OpenPlant Cambridge Coordinator Dr Jenny Molloy appeared on BBC Radio 4's 'Inside Science' last week following the publication of a bioengineering horizon scanning exercise co-organised by the Centre for the Study of Existential Risk and SynBio SRI, (both University of Cambridge) and the Future of Humanity Institute (University of Oxford) in Dec 2016.

In an interview with host Adam Rutherford, Jenny discussed the potential democratised future of synthetic biology and the importance of open tools and technologies for engineering biology, such as those generated by OpenPlant and the SRI's activities such as the Biomaker Challenge.

Topics covered included the ways in which synthetic biology is getting cheaper, faster and more distributed with increasing activity within institutions and education but also in community labs like Cambridge's Biomakespace. Changing ownership models in biotechnology was highlighted in the horizon scan as a long term trend that is likely to be a major issue in the next 15 years; it can potentially lead to greater equity in access to technology for public benefit but democratisation also raises questions of responsible governance and regulation. Jenny pointed to the work of the Woodrow Wilson Centre in demonstrating that the DIY biology community are typically very proactive in self-governance and drawing up community codes of ethics and engaging with law enforcement and regulators.

You can download or take a listen to the episode online. The synthetic biology segment starts at 14 min.

More information on the biological engineering horizon scan >>

Wintle, Bonnie C., Christian R. Boehm, Catherine Rhodes, Jennifer C. Molloy, Piers Millett, Laura Adam, Rainer Breitling et al. "A transatlantic perspective on 20 emerging issues in biological engineering." eLife 6 (2017).

[Closes 31 Dec 2017] Applications for the 2018 EUSynBioS Steering Committee are now open !

EUSynBioS is a community for students and postdocs in European synthetic biology. Applications to join their 2018 Steering Committee are now open until 31 December 2017, where you can help facilitate horizontal connections across the synthetic biology community and convene joint events with fellow communities around the globe.

Christian Boehm, who recently completed his PhD at the University of Cambridge is the current EUSynBioS Chair and sends this message:

"Dear EUSynBioS community,

As you know, this initiative is run entirely by dedicated students and postdocs keen to make a difference in European synthetic biology. Over the previous year, we have had a fantastic group of people on the Steering Committee: they have amplified our social media presence, represented our voice in the UN Convention on Biological Diversity's discussions on synthetic biology, organised the EUSynBioS Social in Manchester and of course our EUSynBioS Symposium at CNB-CSIC Madrid.
The fourth year of EUSynBioS shall facilitate horizontal connections across the community, further strengthen our interface to industry, and bring about more joint events with fellow communities around the globe.

Do these challenges sound appealing to you ?
Do you have an idea which would really make a difference to the community ?
Do you have what it takes to be a leader in European synthetic biology ?

Then be a part of the 2018 EUSynBioS Steering Committee!
Applications are now open until 31. December 2017. We will be in touch with you soon thereafter, and aim to announce our 2018 Steering Committee in early January."

More information and to apply >>

Technology for development and design for co-creation workshops

The Cambridge Global Challenges Initiative is running the following events for post-graduates and early career researchers in the New Year and a Global Challenges Round Table on 8th December. Book now to secure your place!

Global Challenges Round Table - 8th December

GCI will run Round Tables twice a year to give Cambridge researchers the opportunity to talk about research relating to the UN Sustainable Development Goals (SDGs). The programme of the December 2017 edition, which includes data-driven modelling of airborne diseases, digital design for development aid and innovative bacterial testing, has been shared. You are still very welcome to register to participate in the discussions that will follow the short talks and/or to share research projects to be presented in forthcoming editions of the Round Tables. 

Co-creation for Global Challenges

The following events are part of the focus of Global Challenges Initiative in facilitating the dialogue and co-creation between Cambridge researchers and end-users in the developing world. 

• • Workshop on User-Centred Design in Developing World Contexts – 10th January (application deadline: 15th December). This workshop will introduce the principles of user-centred design and explore the specific challenges and opportunities that commonly arise when using this approach to co-create innovative responses to global challenges. The workshop is open to post-graduates and early career researchers, from different research backgrounds, interested in user-centred design for the benefit of the bottom half of the world’s population. To apply please send a CV (max. 2 pages) and a letter of motivation outlining your interest and how you hope to apply learnings from the workshop to Sophie Mower (sophie.mower@centreforglobalequality.org). 

• Masterclass in Design Methods for Global Challenges – 11th January. This Masterclass will explore the similarities and differences between particular disciplinary approaches to co-creation with end-users in developing world contexts. One-to-one discussions between expert practitioners from different disciplinary and practitioner communities and established Cambridge researchers in fields within the EPSRC remit will be organized. To register for the event, please complete the online form.

Please note that a Technology for Development Graduate Sandpit – 15th January (application deadline: 11th December), aimed at Graduate students and Early Career Researchers, will take place after these two co-creation-oriented events. Winning teams of the competition sandpit will be awarded bursaries to undertake field trips to develop and test their ideas in real developing world situations. Please apply by completing the application form and submitting a CV (max. 2 pages) to winton@phy.cam.ac.uk.

RebelBio opens call for London life-sciences accelerator - deadline 1 Dec 2017

RebelBio, the world’s first early-stage life-sciences accelerator, is seeking applications from ambitious scientists and entrepreneurs for its 2018 programmes. Science graduates, PhDs, postdocs and academics who feel a strong urge to commercialise their research or who need to advance their existing companies are particularly welcome.

More information from RebelBio 

Our investment  is given with the aim to develop a life-sciences product, commercialise research, or accelerate existing companies that can give the world something it needs.

RebelBio will invest up to $250K*, along with extensive business and scientific mentoring during the three-month period of the program, which take place in London from January 8th to April 8th 2018 & Corks programme from May - July.

During this time, RebelBio will provide laboratory space and supplies designed to allow our founders to move forward technically and business development. The program will culminate with a demo day and is part of an ongoing relationship that applicants will have with the world’s premier early-stage venture-capital fund, SOSV.

This relationship will provide many benefits including access to RebelBio’s vast network of investors, corporates and other like-minded entrepreneurs.

Application Information:

• Apply here - https://goo.gl/jXSzx1
• Review overview deck containing additional information on our programme - https://goo.gl/jXSzx1
• More details - https://goo.gl/XaN4yh

Deadlines:

• The closing date for the London programme is December 1st 2017
• The closing date for the Cork programme will be announced in early 2018.

Informal inquiries through contacting steven.oconnell@sosv.com.  

*Subject to performance

Biomaker Fayre showcases 40 open source, low-cost biological instruments

There was a real buzz in the air on Saturday 21 October, as 40 interdisciplinary teams exhibited their prototypes for the 2017 Biomaker Challenge at the Department of Engineering.

Projects covered everything from spectrometers for measuring the colour of penguin guano, microfluidics for tissue culture, to ultrasonic systems for measuring plant height and 3D printed modular microscopes. Each group was given a £1000 grant and four months to turn their big ideas for open source and DIY research tools into reality and over 100 people came along to the final event.

The Challenge and Fayre aimed to show the value of open, low-cost and DIY technologies as convening points for interactions between biologists and engineers. They are also important educational tools for those who are interested in developing technical skills and have great potential for improving the quality of science and increasing productivity in the lab for lower costs. With the proliferation of digital designs for 3D-printing and easily available consumer electronics like Arduino which has a huge community of users and lots of online help, designing your instrumentation around your experiment rather than vice versa has never been more possible.

Winners of the 3D-printed awards were:

Best Technology: A low-cost chromatography system for protein purification

Stéphanie Polderdijk (Cambridge Institute for Medical Research) and Wolfgang Schmied (MRC LMB) set out to lower the cost of column chromatography: a routine technique for the separation of components from complex mixtures.

In biochemistry and molecular biology, proteins frequently need to be purified by gravity flow, centrifugation, which are time-consuming or by using expensive automated systems that use pumps to force solutions over a column. They produced a lower cost, modular, open-source alternative to these commercial systems for performing simple, routine purifications.

Best Biology: PiRMA: A low-cost rodent physiology monitoring bed for pre-clinical experiments

Marcel Gehrung, Dominick McIntyre and Lina Hacker (all from CRUK Cambridge Institute) developed a low-cost rodent physiology monitor which is suitable for a wide range of experiments and imaging applications such as Magnetic Resonance Imaging (MRI) and Computed Tomography (CT). Parameters such as Heart Rate (HR), Respiratory Rate (RR), and Temperature can be measured which are important to reduce data artefacts. Existing solutions are in the cost range of several thousand pounds and do not support the holistic workflow required in animal experiments.

Maker Spirit: A DIY focus stacking system for macrophotography of developing ferns 

Jennifer Deegan (Department of Plant Sciences) and team Matthew Couchman (John Innes Centre), Tim Deegan (CohoData) and Richard Mortier (Computer Lab) developed a  very low-budget  focus stacking system for microphotography in order to take a series of photographs showing the development of the fern gametophyte from the very earliest feasible stage to the appearance of the first sporophyte leaf. 

Dr Jenny Molloy, co-organiser of the Biomaker Challenge and Fayre reported that “the judging panel were hugely impressed by the progress the teams made over just four months and we're excited to see where people go next with these open source designs, that are free for anyone to download, replicate and build on in their own labs”.

See more photos from the day here >>

Biomaker Challenge 2017 was jointly funded by OpenPlant, a BBSRC/EPSRC Synthetic Biology Research Centre Grant BB/L014130/1 and the Isaac Newton Trust.

The Biomaker Challenge and Biomaker Fayre were coordinated by University of Cambridge's Synthetic Biology Strategic Research Initiative and the CambridgeSens Network.

Thank you also to our sponsors ARM Ltd and New England Biolabs.

Expressions of interest open for BrisSynBio 4 Day MBA (9 - 13 April 2018)

BrisSynBio will be running their successful 4 day MBA again in April 2018 and are likely to be able to offer significantly discounted (or even free) tickets to postdocs and PhD students from the UK Synthetic Biology Research Centres, including OpenPlant

Details of the 2017 course are available here: http://www.bristol.ac.uk/brissynbio/innovation/innovation-training-and-events/

Early expressions of interest should go to Andy Boyce: Andy.Boyce@bristol.ac.uk  

[Closes 24 Nov 2107] Apply now to the OpenPlant Fund!

The OpenPlant Fund is now open to proposals for innovative, open and interdisciplinary projects relevant to plant or in vitro Synthetic Biology. Projects run for six months and can include biological research, hardware prototyping, software, outreach, policy work and training.

For this round applications focused on training and knowledge exchange are especially encouraged.

The deadline is 24 Nov 2017 for projects led from University of Cambridge or Norwich Research Park with external collaborators welcome.

Apply now by 24 Nov 2017 >>>

Download: Poster | Info Sheet

Each successful project will receive up to £5k, with £4k up front and an additional £1k for follow-on and outreach after reporting. PhD students and postdocs are particularly encouraged to apply.
 
A wealth of tools, technologies and methodologies have been developed for plant and cell free Synthetic Biology, including those developed through OpenPlant, the OpenPlant Fund, the Biomaker Challenge and complementary efforts. In the current OpenPlant Fund call, we are encouraging applications for projects that will provide training or knowledge exchange to broaden the use of plant and cell-free synthetic biology tools, techniques and technologies. Information about previous OpenPlant Fund projects are available on www.biomaker.org.
 
For more information see https://www.openplant.org/fund/ and join the upcoming mixer event on Thursday 9 Nov 2017. If you are interested in submitting a proposal or have any questions, please email colette.matthewman@jic.ac.uk.
 

Want to learn more and find collaborators?

OpenPlant Fund mixer and a light-hearted look at training!
4pm on Thursday 9 November, The Rec Centre Bar, John Innes Centre, Norwich
RSVP to this event here >>
 
This event provides an introduction to the opportunities and a chance to present your initial proposals and to meet potential collaborators over drinks and pizza. We will also have a light-hearted look at training, including different models and effective communication of technical details. Come along to learn some tips and tricks in this fun and informative training session, and to network and meet potential collaborators. More details to follow.

Cafe Synthetique: Towards engineering circadian rhythms
6pm on Monday 20 November, The Panton Arms, 43 Panton Street, Cambridge
RSVP to this event here >>

Help will be on hand to answer any questions you might have as the deadline for applications approaches and to find last minute partners for your teams!
 

Eligibility

Applicants should be graduate students or postdoctoral workers at the University of Cambridge, the John Innes Centre or The Sainsbury Laboratory. The team must be interdisciplinary, must contain members from both Norwich and Cambridge and may contain external collaborators of any type. Applicants must have agreement from their research supervisor and cost-code sponsor that the proposed project and management of the allocated funding will fit with their existing work. All proposals must lead to tangible, publicly documented and open outcomes, which could include (but are not limited to) the following:

• Design files and prototype for a hardware project
• Software development and documentation
• White paper arising from a workshop
• Educational resource
• Synthesis and sharing of useful DNA parts or vectors.

For more information and to apply see the OpenPlant Fund webpage

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

Former OpenPlant Fellow Dr Fernan Federici, former OpenPlant PDRA Dr Tim Rudge and colleagues have recently published a pre-print for their low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering, supported by the OpenPlant Fund.

Nuñez, Isaac, Tamara Matute, Roberto Herrera, Juan Keymer, Tim Marzullo, Tim Rudge, and Fernan Federici. "Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering." bioRxiv (2017): 194324

Examples of images of bacterial colonies and cell-free systems using the microscope. Credit: Federici Lab

Abstract

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates.

We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information.

To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential for STEM teaching in a high school environment, using it to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for STEM education, scientific research and bioengineering. All the resources developed here are available under open source license

[Closes 30 Nov 2017] GapSummit 2018 open for applications

GapSummit is 'The world’s first global and intergenerational leadership summit in biotechnology' from Global Biotech Revolution and will take place 16-18 April 2018 at St Johns College, Cambridge.

The GapSummit welcomes 100 future bio-leaders (Leaders of Tomorrow) from around the world for a 3-day conference, which aims to "provide the bio-leaders of tomorrow with a comprehensive overview of current and future biotechnology trends and issues, inciting discussion about world challenges that can be met by biotechnological application."

 The GapSummit 2018 will attract more than 60 world leaders and pioneers from the biotech, pharmaceutical & healthcare industry to the University of Cambridge.

APPLY NOW

Deadline 30 Nov 2017

Cafe Synthetique tackles DNA-based Information Storage and DNA Synthesis

Cafe Synthetique on 18 Sep 2017 commanded a full house with plenty of interesting discussion around Pierre Murat's research on DNA-based information storage and Jiahao Huang's work on long chain DNA synthesis.

Pierre Murat from the Department of Chemistry spoke about his research on encoding and decoding synthetic strands of DNA. He presented data to show how he turned (the encoded word) 'Black to 'White', Pierre has also successfully encoded images of Darwin ,Franklin and and Turin! By exploiting differential kinetics of hydrolytic deamination reactions of cytosine and its naturally occurring derivatives, he demonstrated how multiple layers of information can be stored in a single DNA template. He explained how controlled redox reactions allow for interconversion of these DNA-encoded layers of information, encoding a single strand with multiple 'messages'.

Discussion focussed in part, on the challenges of sequencing the complex encoded DNA, including the ultimate test: an outsider successfully decoding a message hidden in DNA from Murat's lab - a challenge many attendees might relish.

Jiahao Huang covered the interesting history of DNA synthesis since it's advent in the 1970's before talking about the exciting work going on at Nuclera Nucleics where heand his colleaguesare developing a next-generation DNA synthesis using engineered terminal deoxynucleotidyl transferases, or TdT. With tehability to synthesise strands tens of bases long already, he hopes to be able to accurately produce long chain DNA strands by the end of this decade, and ultimately whole genomes. Discussion covered, accuracy, large scale production and lead to the inevitable question of cost. With research moving at a rapid pace Jiahao anticipates that a long chain sample will eventually become less than the cost of sending it by FedEx!

OpenPlant Fund supported project publishes on better DNA transfer from Escherichia coli to Bacillus subtilis

Dr Mario Juhas and OpenPlant PI  Dr Jim Ajioka from the Department of Pathology at the University of Cambridge have contributed to creating reliable and efficient systems for the transfer of synthetic DNA between E. coli and B. subtilis, supported by the OpenPlant Fund.

The majority of the good DNA editing techniques have been developed in Escherichia coli; however, Bacillus subtilis is better host for a plethora of synthetic biology and biotechnology applications. 

Using synthetic biology approaches, such as streamlined lambda Red recombineering and Gibson Isothermal Assembly, the team integrated genetic circuits  encoding the lysis genes of bacteriophages MS2, ΦX174 and lambda, the thermosensitive repressor and the T7 RNA polymerase into the E. coli chromosome.

In this system the T7 RNA polymerase regulated by the thermosensitive repressor drives the expression of the phage lysis genes. T7 RNA polymerase significantly increases efficiency of cell lysis and transfer of the plasmid and bacterial artificial chromosome-encoded DNA from the lysed E. coli into B. subtilis. The T7 RNA polymerase-driven inducible cell lysis system is therefore suitable for the efficient cell lysis and transfer of the DNA engineered in E. coli to other naturally competent hosts, such as B. subtilis.

The research obtained support from the SynBio Fund and OpenPlant Fund

The full article can be read here.

Image attribution: Debivort at the English language Wikipedia
This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.

Cafe Synthetique highlights graduate student work in synthetic biology: algae, arsenic testing and automated labs

Cafe Synthetique this August gave the floor to a talented collection of graduate students working on synthetic biology projects around the University of Cambridge and primarily from OpenPlant Labs. It was an excellent insight into some cutting edge science and how these early career researchers view the future of biological engineering.

Jan Lyczakowski (Department of Biochemistry) from Prof Paul Dupree’s lab described his efforts to engineer the structure of the plant sugar xylan in order to extract more biofuel from woody biomass. By using an enzyme from the plant model organism Arabidopsis thaliana, several times more xylose sugar could be extracted and fermented into ethanol using engineered E.coli bacteria. Jan also brought along some 3D-printed models of xylan to provide a hands-on demonstration of the structure!

Algal synthetic biology featured heavily as Aleix Gorchs Rivera, Stefan Grossfurthner and Patrick Hickland from Prof Alison Smith’s Lab, in the Department of Plant Sciences, presented different approaches to engineering algae to generate valuable products, such as pigments and medicinal compounds.

Patrick’s work focuses on tools to engineer the brown alga Phaeodactylum tricornutum, which is not a common lab organism but has useful features like a rapid growth rate and high accumulation of lipids like omega 3 fatty acids. Specifically, Patrick has engineered an inducible on/off genetic switch in the alga and is now applying it to manipulate metabolic pathways and boost production of useful compounds.

Aleix and Stefan are both working with the more common model alga Chlamydomonas reinhardtii. Aleix presented his work building inducible genetic circuits to express in the algal chloroplast, which is a major site of protein production. He aims to tightly dose expression of interesting metabolic genes and even antibodies. Stefan is constructing a metabolic pathway for engineering and manipulating cytosolic production of sesquiterpenes, an interesting family of compounds including the anti-malarial drug artemisinin. He presented his current progress during the first year of his PhD and future plans.

From eukaryotes to cell-free biochemical systems, Tess Skyrme represented the Sensors Centre for Doctoral Training (Department of Chemical Engineering and Biotechnology), where 12 students have spent the summer designing and prototyping an arsenic biosensor. Their sensor produces glucose oxidase in the presence of arsenic which is detected electrochemically on a device that can send data from remote field locations such as wells in Bangladesh and Nepal, where arsenic contamination has been described as the ‘largest mass poisoning of a population in history’ (WHO, 2002). The team built an arsenic sensitive genetic circuit, tested multiple electrochemistries, and designed an open source potentiometer that is 10% the cost of commercially available options for almost equivalent functionality. They are now focused on integrating the device components ahead of Sensors Day on 20 Oct 2017.

Looking to the future and calling for a revolution in the way that biological experiments are performed, Clayton Rabideau provided an introduction to the current state of the art in machine learning and automation in synthetic biology. His presentation marked the first appearance of Mario Brothers at Cafe Synthetique, with a demonstration of how machine learning over many generations can result in large efficiency gains compared.

Efficiency was also a key driver for the increase in labs moving to automated liquid handling through open source lab robots like OpenTrons, new technologies such as the Labcyte Echo, which is available in Cambridge as part of the OpenPlant Synthetic Biology Centre, and fully automated ‘cloud labs’. However, Clayton also highlighted the ‘reproducibility crisis’ in experimental science and how increased use of machines to minimise human error might help. He ended by predicting that in the coming decades graduate students would spend far less time in the lab. This went down well with an audience whose most automated lab experience so far was reportedly ‘multi-channel pipettes’.

It’s the first time that Cafe Synthetique has featured a full line up of graduate students and we hope to repeat the successful format in the near future. If you are a graduate student working on a synthetic biology related topic and would like to present at the next Cafe Synthetique Grad Talks, get in touch!

New Royal Society Report: Synthetic Biology - does industry get it?

On 8 February 2017, the Royal Society hosted a conference that posed the question Synthetic biology – does industry get it? It brought together nearly 200 experts from academia, industry and government to provide an honest and open appraisal of how industry is using synthetic biology, acknowledging successes and strengths but also looking at what barriers still need to be overcome.

A report from the meeting has now been published, summarising the discussions that took place and the key points raised.

Issues including the global energy challenge, regulation and public acceptance of synthetic biology, and finding the right talent and skills were all raised and great industrial interest in synthetic biology was demonstrated.

In answer to the question, “Does industry get it?”, the Royal Society report that:

"there was a clear sense that industry is very interested in synthetic biology but that there remains a conservativism that holds back its wider implementation. Industry speakers encouraged synthetic biologists to look at solving the unmet needs of industry and demonstrate the benefits that future products will bring. Researchers should avoid the risk of overselling their new and exciting science - there needs to be a balance between ambitious, long-term scientific targets and working within the existing product development lifetimes in industry...Synthetic biology stands on the cusp – as the costs of processes fall, the moment where rapid growth in industrialisation will take place is nearly upon us."

The full report can be read here.

Commentary on a Major Advance in Plastid Transformation

OpenPlant PI Professor Julian Hibberd (Department of Plant Sciences, University of Cambridge) has summarised advances towards efficient plastid transformation in Arabidopsis thaliana as part of a new paper in Plant Physiology

This commentary follows 'Efficient Plastid Transformation in Arabidopsis' reported by Pal Maliga's team in this month's Plant Physiology, which could be regarded as a major advance in plastid transformation. Stable manipulation of the plastid genome of flowering plants was first reported nearly 30 years agoby Svab et al. However, for key species including cereal crops including Arabidopsis (Arabidopsis thaliana), the spectinomycin-based approach using the addition of the aadA gene has proved ineffective.

Hibberd cites Parker et al who showed that ecotypes of Arabidopsis vary in their sensitivity to spectinomycin due to the mutant allele of the nuclear gene ACC2. Its product is targeted to plastids and so provides an alternate to the partially plastid-encoded acetyl-Coenzyme A carboxylase that is inactivated by spectinomycin. Parker et al. proposed that their findings may provide a route to increase efficiency of chloroplast transformation in the Brassicaceae.

Yu et al. (2017) now provide strong support for this conjecture showing that by removing redundancy afforded by ACC2, efficient selection for transplastomic events can be achieved in Arabidopsis.

The next challenge is therefore to identify procedures and ecotypes that facilitate this conversion of transplastomic callus of Arabidopsis into stable and heritable plant material.

Hibberd's full commentary can be read here.

Call for exhibits at Biomaker Fayre 2017

Biomaker Fayre 2017 will include demonstrations of open source biological instruments, lab and field equipment featuring over 40 teams who participated in the 2017 Biomaker Challenge. All others with maker projects related to science and biology are invited to exhibit! We'll have everything from spectrometers for measuring the colour of penguin guano, microfluidics for tissue culture, to ultrasonic systems for measuring plant height and 3D printed modular microscopes.

There'll also be some fantastic talks just before at the Open Technology Workshop. COme and learn about everything from distributed 3D printing in Africa, open hardware in Brazil and universities collaborating with companies to create open technologies in Denmark. 

Want to exhibit?

• Please do! Biomaker Fayre exhibitors can attend the Open Technology Workshop free of charge.
• Every individual exhibitor should register using the esales form under 'concessions'
• Each exhibit must also complete an exhibit registration form

For more information and the schedule take a look at the Open Technology webpage

OpenPlant researchers publish a strategy to improve conversion of plant biomass to sugars for bioenergy

A new publication from the lab of OpenPlant PI Prof. Paul Dupree, University of Cambridge in Biotechnology for Biofuels describes work to improve processing of softwood to biofuels using a synthetic biology strategy to express and assay conifer cell wall synthesis enzymes.

Lyczakowski, J.J., Wicher, K.B., Terrett, O.M., Faria-Blanc, N., Yu, X., Brown, D., Krogh, K.B.R.M., Dupree, P., and Busse-Wicher, M. (2017). Removal of glucuronic acid from xylan is a strategy to improve the conversion of plant biomass to sugars for bioenergy. Biotechnology for Biofuels 10: 224

Abstract

Background: Plant lignocellulosic biomass can be a source of fermentable sugars for the production of second generation biofuels and biochemicals. The recalcitrance of this plant material is one of the major obstacles in its conversion into sugars. Biomass is primarily composed of secondary cell walls, which is made of cellulose, hemicelluloses and lignin. Xylan, a hemicellulose, binds to the cellulose microfibril and is hypothesised to form an interface between lignin and cellulose. Both softwood and hardwood xylan carry glucuronic acid side branches. As xylan branching may be important for biomass recalcitrance and softwood is an abundant, non-food competing, source of biomass it is important to investigate how conifer xylan is synthesised.

Results: Here, we show using Arabidopsis gux mutant biomass that removal of glucuronosyl substitutions of xylan can allow 30% more glucose and over 700% more xylose to be released during saccharification. Ethanol yields obtained through enzymatic saccharification and fermentation of gux biomass were double those obtained for non-mutant material. Our analysis of additional xylan branching mutants demonstrates that absence of GlcA is unique in conferring the reduced recalcitrance phenotype. As in hardwoods, conifer xylan is branched with GlcA. We use transcriptomic analysis to identify conifer enzymes that might be responsible for addition of GlcA branches onto xylan in industrially important softwood. Using a combination of in vitro and in vivo activity assays, we demonstrate that a white spruce (Picea glauca) gene, PgGUX, encodes an active glucuronosyl transferase. Glucuronic acid introduced by PgGUX reduces the sugar release of Arabidopsis gux mutant biomass to wild-type levels indicating that it can fulfil the same biological function as native glucuronosylation.

Conclusion: Removal of glucuronic acid from xylan results in the largest increase in release of fermentable sugars from Arabidopsis plants that grow to the wild-type size. Additionally, plant material used in this work did not undergo any chemical pretreatment, and thus increased monosaccharide release from gux biomass can be achieved without the use of environmentally hazardous chemical pretreatment procedures. Therefore, the identification of a gymnosperm enzyme, likely to be responsible for softwood xylan glucuronosylation, provides a mutagenesis target for genetically improved forestry trees.